Major Histocompatibility Complex (MHC) encodes a group of closely linked genes that play a central role in the vertebrate immune system, those are crucial for understanding the influence of natural selection on genetic diversity in wild populations. We examined genetic variation at the MHC class II DRB gene in 15 sampled localities of the Jamaican fruit-eating bat (Artibeus jamaicensis) in Mexico. Artibeus jamaicensis is one of the most abundant and widely distributed species in the Neotropics, and is therefore an excellent species in which to examine immunological gene variation. Using PCR amplifications, cloning and sequencing, we assessed individual DRB allelic diversity. Sequences from 193 individuals were analyzed and no deletions or insertions were detected, thus likely representing functional alleles. We identified 161 alleles (allele diversity = 0.9789 0.0022), with three to five alleles per individual, suggesting gene duplication events. Our results suggest the presence of recombination involved with generating DRB diversity in A. jamaicensis; we detected one recombination breakpoint and one recombination event. In the antigen-binding site (ABS), the average number of nonsynonymous substitutions per site is greater than the synonymous substitutions per site (0.7033 versus 0.2966, respectively) providing evidence for positive selection acting above the evolutionary history of the species in shaping MHC diversity.